Bleeding disorders can be characterized by excessive blood clotting known as thrombosis, or by the inability to form blood clots termed hemophilia. Blood clotting is a tightly regulated process involving exquisite control of the many proteins in the blood clotting cascade including factor IXa, factor VIIIa, factor Xa, and factor VIIa. We are working to understand the structural determinants of the regulation of factor IXa, a central protein in the clotting cascade. The activation of factor IXa results in clotting whereas the inhibition prevents clotting. Better understanding of the structure of factor IXa will lead to the design of small protein mimetics to treat blood clotting disorders. The catalytic activity of factor IXa is dependent on a cofactor called factor VIIIa. We are working on determining the structure of factor IXa with factor VIIIa in order to elucidate the structural determinants leading to the activation of factor IXa. Further, ecotin, a serine protease inhibitor, will be derivatized to specifically inhibit factor IXa. Inhibition of factor IXa is expected to protect against thrombosis without resulting bleeding complications which is expected from inhibiting factor Xa or factor VIIa. The crystallographic analysis of factor IXa-ecotin derivatives will facilitate our understanding of the region(s) of ecotin which are important for the inhibition of factor IXa. I am using the Computer Graphics Laboratory and MidasPlus to structurally model factor IXa with factor VIIIa and ecotin derivatives.